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Establishment and Preliminary Characterization of Three Astrocytic Cells Lines Obtained from Primary Rat Astrocytes by Sub-Cloning. Genes (Basel) 2020; 11:genes11121502. [PMID: 33322092 PMCID: PMC7764261 DOI: 10.3390/genes11121502] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 12/07/2020] [Accepted: 12/11/2020] [Indexed: 01/10/2023] Open
Abstract
Gliomas are complex and heterogeneous tumors that originate from the glial cells of the brain. The malignant cells undergo deep modifications of their metabolism, and acquire the capacity to invade the brain parenchyma and to induce epigenetic modifications in the other brain cell types. In spite of the efforts made to define the pathology at the molecular level, and to set novel approaches to reach the infiltrating cells, gliomas are still fatal. In order to gain a better knowledge of the cellular events that accompany astrocyte transformation, we developed three increasingly transformed astrocyte cell lines, starting from primary rat cortical astrocytes, and analyzed them at the cytogenetic and epigenetic level. In parallel, we also studied the expression of the differentiation-related H1.0 linker histone variant to evaluate its possible modification in relation with transformation. We found that the most modified astrocytes (A-FC6) have epigenetic and chromosomal alterations typical of cancer, and that the other two clones (A-GS1 and A-VV5) have intermediate properties. Surprisingly, the differentiation-specific somatic histone H1.0 steadily increases from the normal astrocytes to the most transformed ones. As a whole, our results suggest that these three cell lines, together with the starting primary cells, constitute a potential model for studying glioma development.
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Caradonna F, Cruciata I, Schifano I, La Rosa C, Naselli F, Chiarelli R, Perrone A, Gentile C. Methylation of cytokines gene promoters in IL-1β-treated human intestinal epithelial cells. Inflamm Res 2017; 67:327-337. [PMID: 29256007 DOI: 10.1007/s00011-017-1124-5] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2017] [Revised: 12/13/2017] [Accepted: 12/13/2017] [Indexed: 12/23/2022] Open
Abstract
OBJECTIVE AND DESIGN Epigenetic regulation is important in the activation of inflammatory cells. In the present study, we evaluated if DNA-methylation variations are involved in Interleukin-1β (IL-1β)-induced intestinal epithelial cells activation. MATERIALS AND METHODS Differentiated Caco-2 cells were exposed to IL-1β or to 5-azadeoxycytidine (5-azadC) for 24 or 48 h. Genome-wide methylation status was evaluated, while DNA methylation status at the promoter region of the gene encoding interleukin-6, 8 and 10 (IL-6, 8 and 10) was estimated. The levels of the corresponding gene products as well as DNA methyltransferases (DNMTs) quantity were assessed. RESULTS IL-1β decreased genomic methylation of human intestinal epithelial cells and induced demethylation at cg-specific sites at the promoter of pro-inflammatory genes IL6 and IL8; conversely it did not change the methylation of the IL10 promoter. IL-1β also increased the release of IL-6 and IL-8 but did not change the IL-10 expression. Finally, cell exposure to IL-1β decreased the DNMT3b expression, increased DNMT3a and was not able to change DNMT1 expression. CONCLUSIONS Our results suggest a potential role of IL-1β as modulator of DNA methylation in activated differentiated Caco-2 cell line.
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Affiliation(s)
- Fabio Caradonna
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF, Sezione di Biologia cellulare), Università di Palermo, Viale delle Scienze, Edificio 16, 90128, Palermo, Italy
| | - Ilenia Cruciata
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF, Sezione di Biologia cellulare), Università di Palermo, Viale delle Scienze, Edificio 16, 90128, Palermo, Italy
| | - Ilaria Schifano
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF, Sezione di Biologia cellulare), Università di Palermo, Viale delle Scienze, Edificio 16, 90128, Palermo, Italy
| | - Chiara La Rosa
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF, Sezione di Biologia cellulare), Università di Palermo, Viale delle Scienze, Edificio 16, 90128, Palermo, Italy
| | - Flores Naselli
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF, Sezione di Biologia cellulare), Università di Palermo, Viale delle Scienze, Edificio 16, 90128, Palermo, Italy
| | - Roberto Chiarelli
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF, Sezione di Biologia cellulare), Università di Palermo, Viale delle Scienze, Edificio 16, 90128, Palermo, Italy
| | - Anna Perrone
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF, Sezione di Biologia cellulare), Università di Palermo, Viale delle Scienze, Edificio 16, 90128, Palermo, Italy
| | - Carla Gentile
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF, Sezione di Biologia cellulare), Università di Palermo, Viale delle Scienze, Edificio 16, 90128, Palermo, Italy.
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Barros AV, Wolski MAV, Nogaroto V, Almeida MC, Moreira-Filho O, Vicari MR. Fragile sites, dysfunctional telomere and chromosome fusions: What is 5S rDNA role? Gene 2017; 608:20-27. [DOI: 10.1016/j.gene.2017.01.013] [Citation(s) in RCA: 49] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Revised: 01/04/2017] [Accepted: 01/18/2017] [Indexed: 11/29/2022]
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Locati MD, Pagano JFB, Ensink WA, van Olst M, van Leeuwen S, Nehrdich U, Zhu K, Spaink HP, Girard G, Rauwerda H, Jonker MJ, Dekker RJ, Breit TM. Linking maternal and somatic 5S rRNA types with different sequence-specific non-LTR retrotransposons. RNA (NEW YORK, N.Y.) 2017; 23:446-456. [PMID: 28003516 PMCID: PMC5340908 DOI: 10.1261/rna.059642.116] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2016] [Accepted: 12/03/2016] [Indexed: 05/31/2023]
Abstract
5S rRNA is a ribosomal core component, transcribed from many gene copies organized in genomic repeats. Some eukaryotic species have two 5S rRNA types defined by their predominant expression in oogenesis or adult tissue. Our next-generation sequencing study on zebrafish egg, embryo, and adult tissue identified maternal-type 5S rRNA that is exclusively accumulated during oogenesis, replaced throughout the embryogenesis by a somatic-type, and thus virtually absent in adult somatic tissue. The maternal-type 5S rDNA contains several thousands of gene copies on chromosome 4 in tandem repeats with small intergenic regions, whereas the somatic-type is present in only 12 gene copies on chromosome 18 with large intergenic regions. The nine-nucleotide variation between the two 5S rRNA types likely affects TFIII binding and riboprotein L5 binding, probably leading to storage of maternal-type rRNA. Remarkably, these sequence differences are located exactly at the sequence-specific target site for genome integration by the 5S rRNA-specific Mutsu retrotransposon family. Thus, we could define maternal- and somatic-type MutsuDr subfamilies. Furthermore, we identified four additional maternal-type and two new somatic-type MutsuDr subfamilies, each with their own target sequence. This target-site specificity, frequently intact maternal-type retrotransposon elements, plus specific presence of Mutsu retrotransposon RNA and piRNA in egg and adult tissue, suggest an involvement of retrotransposons in achieving the differential copy number of the two types of 5S rDNA loci.
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Affiliation(s)
- Mauro D Locati
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Johanna F B Pagano
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Wim A Ensink
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Marina van Olst
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Selina van Leeuwen
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Ulrike Nehrdich
- Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories - Cell Observatorium, Leiden 2333 CE, The Netherlands
| | - Kongju Zhu
- Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories - Cell Observatorium, Leiden 2333 CE, The Netherlands
| | - Herman P Spaink
- Department of Molecular Cell Biology, Institute of Biology, Leiden University, Gorlaeus Laboratories - Cell Observatorium, Leiden 2333 CE, The Netherlands
| | - Geneviève Girard
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Han Rauwerda
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Martijs J Jonker
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Rob J Dekker
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
| | - Timo M Breit
- RNA Biology & Applied Bioinformatics Research Group, Swammerdam Institute for Life Sciences, Faculty of Science, University of Amsterdam, Amsterdam 1090 GE, The Netherlands
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Tyunin AP, Ageenko NV, Kiselev KV. Effects of 5-azacytidine-induced DNA demethylation on polyketide synthase gene expression in larvae of sea urchin Strongylocentrotus intermedius. Biotechnol Lett 2016; 38:2035-2041. [DOI: 10.1007/s10529-016-2191-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Accepted: 08/18/2016] [Indexed: 10/21/2022]
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Bellavia D, Dimarco E, Caradonna F. Characterization of three different clusters of 18S-26S ribosomal DNA genes in the sea urchin P. lividus: Genetic and epigenetic regulation synchronous to 5S rDNA. Gene 2016; 580:118-124. [PMID: 26789074 DOI: 10.1016/j.gene.2016.01.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2015] [Revised: 01/07/2016] [Accepted: 01/08/2016] [Indexed: 01/23/2023]
Abstract
We previously reported the characterization 5S ribosomal DNA (rDNA) clusters in the common sea urchin Paracentrotus lividus and demonstrated the presence of DNA methylation-dependent silencing of embryo specific 5S rDNA cluster in adult tissue. In this work, we show genetic and epigenetic characterization of 18S-26S rDNA clusters in this specie. The results indicate the presence of three different 18S-26S rDNA clusters with different Non-Transcribed Spacer (NTS) regions that have different chromosomal localizations. Moreover, we show that the two largest clusters are hyper-methylated in the promoter-containing NTS regions in adult tissues, as in the 5S rDNA. These findings demonstrate an analogous epigenetic regulation in small and large rDNA clusters and support the logical synchronism in building ribosomes. In fact, all the ribosomal RNA genes must be synchronously and equally transcribed to perform their unique final product.
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Affiliation(s)
- Daniele Bellavia
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Sezione di Biologia Cellulare, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy; Laboratorio di Ingegneria Tissutale, Istituto Ortopedico Rizzoli, c/o Dipartimento di Biopatologia e Biotecnologie Mediche e Forensi (DIBIMEF), Università di Palermo, Via Divisi, 81, 90133 Palermo, Italy.
| | - Eufrosina Dimarco
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Sezione di Biologia Cellulare, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
| | - Fabio Caradonna
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Sezione di Biologia Cellulare, Università degli Studi di Palermo, Viale delle Scienze, 90128 Palermo, Italy
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Naselli F, Catanzaro I, Bellavia D, Perez A, Sposito L, Caradonna F. Role and importance of polymorphisms with respect to DNA methylation for the expression of CYP2E1 enzyme. Gene 2013; 536:29-39. [PMID: 24333271 DOI: 10.1016/j.gene.2013.11.097] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2013] [Revised: 11/10/2013] [Accepted: 11/25/2013] [Indexed: 12/26/2022]
Abstract
Different individuals possess slightly different genetic information and show genetically-determined differences in several enzyme activities due to genetic variability. Following an integrated approach, we studied the polymorphisms and methylation of sites contained in the 5' flanking region of the metabolizing enzyme CYP2E1 in correlation to its expression in both tumor and non-neoplastic liver cell lines, since to date little is known about the influence of these (epi)genetic elements in basal conditions and under induction by the specific inductor and a demethylating agent. In treated cells, reduced DNA methylation, assessed both at genomic and gene level, was not consistently associated with the increase of enzyme expression. Interestingly, the Rsa/Pst haplotype differentially influenced CYP2E1 enzyme expression. In addition, regarding the Variable Number of Tandem Repeats polymorphism, cells with A4/A4 genotype showed a greater expression inhibition (ranging from 20% to 30%) compared with others carrying the A2/A2 one, while those cells bringing A2/A3 genotype showed an increase of expression (of 25%, about). Finally, we demonstrated for the first time that the A2 and A3 CYP2E1 alleles play a more important role in the expression of the enzyme, compared with other (epi)genetic factors, since they are binding sites for trans-acting proteins.
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Affiliation(s)
- Flores Naselli
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Sezione di Biologia Cellulare, Edificio 16, Università di Palermo, V.le delle Scienze, 90128 Palermo, Italy
| | - Irene Catanzaro
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Sezione di Biologia Cellulare, Edificio 16, Università di Palermo, V.le delle Scienze, 90128 Palermo, Italy
| | - Daniele Bellavia
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Sezione di Biologia Cellulare, Edificio 16, Università di Palermo, V.le delle Scienze, 90128 Palermo, Italy; Istituto Ortopedico Rizzoli, c/o Dipartimento di Biopatologia e Biotecnologie Mediche e Forensi (DIBIMEF), Università di Palermo, Via Divisi, 81, 90133 Palermo, Italy
| | - Alessandro Perez
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Sezione di Biologia Cellulare, Edificio 16, Università di Palermo, V.le delle Scienze, 90128 Palermo, Italy
| | - Laura Sposito
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Sezione di Biologia Cellulare, Edificio 16, Università di Palermo, V.le delle Scienze, 90128 Palermo, Italy
| | - Fabio Caradonna
- Dipartimento di Scienze e Tecnologie Biologiche Chimiche e Farmaceutiche (STEBICEF), Sezione di Biologia Cellulare, Edificio 16, Università di Palermo, V.le delle Scienze, 90128 Palermo, Italy.
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